The scientific community has moved on from Whittaker's Five Kingdom classification system that you and I learnt in school. Cavalier-Smith, in 1998, proposed a "Revised Six Kingdom System" in which all botanical life was classified into Kingdoms Fungi, Plantae and Chromista, zoological species into Protozoa and Animalia, while Bacteria were awarded their own kingdom (Cavalier-Smith,1998). In an earlier paper, he proposed 18 phyla under the Kingdom Protozoa, of which Phylum Apicomplexa was but one.
Other classification styles developed before this time, rule that the three phyla Apicomplexa, Dinozoa (Dinoflagellates) and Ciliophora (Ciliates like Paramecium) must be grouped together under the monophyletic group Alveolata. All members have a subsurface alveoli, microtubules, mitophores and mitochondria with ampulliform or tubular cristae. (Adl et al.,2005)
Cavalier-Smith proposed that the phylum Apicomplexa be further subdivided into two subphyla : Apicomonada and Gamontozon, the latter of which is divided into "infraphylum" Sporozoa (whose members have nine singelet centrioles, complete conoids and conidial rings and the general presence of oocysts and sporocysts in their life cycles) and infraphylum Hematozoa (whose members have a more primitive centriole and lack the presence of oocysts and sporocysts, instead undergoing merogony in vertebrate erythrocytes and gametogony in arthropod guts). (Cavalier-Smith,1993)
In his letter, Cox suggests that based on new analysis Apicomonada has lost its supposed relatedness to the other Apicomplexans (which certainly is true, because it had initially contained only mollusc parasites), and so Sporozoa must be restored to Phylum status (Cox, 2002). This suggestion was apparently not widely accepted, as proved by latter scientific articles that still call the phylum Apicomplexa. Textbooks including popular ones like 'Georgis' Parasitology for Veterinarians' get around this dilemma by adding 'Sporozoa' in parentheses after 'Apicomplexa'.
The traditional grouping of the Apicomplexans, on the basis of phenotype, host, tissue and vector, has been under four broad categories : Coccidians, Gregarines, Haemosporidians and Piroplasms.Each of the groups are defined below:
Coccidia : "host specific, intracellular parasites of the intestines and other organs, of vertebrates with alternating asexual and sexual phases of development resulting in the production of environmentally resistant oocysts in the feces of definitive hosts" (Barta , 2009)
Gregarines : " extra/intra cellular protozoan parasites with large mature gamonts that develop extracellularly with most exhibiting syzygy in their developmental cycles" (Barta , 2009)
Hemosporidians : "obligate heteroxenous blood parasites that undergo sexual development in Dipteran flies and asexual development in vertebrate host" (Dimitrov, 2013)
Piroplasms : Pleomorphic, heteroxenous with an incomplete apical complex; lacks an oocyst stage and flagella (Adl,2005)
Molecular phylogenetic analysis has only added to the confusion by suggesting corrections to canonical taxonomic nomenclature, that is more often not followed by others save the original authors of scientific papers. In the midst of this melee, Cryptosporidium occupies an unique phylogenetic niche. It does not exhibit the cellular vampirism exhibited by the dinoflagellates and gregarines, does not possess variant surface proteins and lacks an apicoplast (a genome- containing plastid-like organelle, homologous to chloroplasts). Analysis of the small subunit ribosomal RNA suggests that the genus is more closely related to the Archigregarines than the Coccidians, but still forms its own clade. With the Archigregarines, Cryptosporidium shares these important characters : monoxenous life cycle, oocyts with four sporozoites, a usual location in the host gastrointestinal tract and extracellular gamonts or trophozoites. (Barta , 2006)
The Tree of Life Web Project has the following "hypothetical tree" for the phylum Apicomplexa showing the major branches viz. clades:
At long last, we come to the real problem. The real question. If taxonomy is so inconstant, how will we/one study diversity and (dare I say it) evolution? There has been a clamour for a taxonomic scheme that will reflect phylogeny.
With this in mind, Morrison D. in a paper titled "Prospects for elucidating the phylogeny of Apicomplexa" lists five important changes that need to occur before any useful, directed progress can be made.
1. Taxon sampling
Anthropocentric research driven by economics and the relative veterinary-medical interest of the parasite has resulted in small, biased sample-data that do not adequately define the boundaries of taxa. Genebank is chock full of Plasmodium, Cryptosporidium, Theileria, Babesia and Toxoplasma sequences, whilst the Eimeria, Sarcocystis, Isospora and Gregarina have few to no representatives. Morrison also states that outgroups and basal taxa must be better studied to help classify already known species into clades.
The accusation of skewed sampling seems quite true. A search on NCBI revealed that as of today (6 Jan 2014), only 47 Apicomplexan species (of the many thousands that exist) have had their complete genome sequenced. All these are virulent parasites of animals/man.
2. Multiple molecular data sets
Frequently, trees are constructed on the basis of one gene (Quite simply because whole genomes are not available to play around with). Such trees, however, are not a true reflection of the relationship between species and clades. Among the Apicomplexans, the 18rRNA gene is most studied. But this gene is most prone to variation in terms of copy number. Other genes commonly studied are the HSP70, Actin, and a few mitochondrial genes. Morrison suggests that analyses be made with multiple gene sets, making sure that both nuclear and organellar genes (the latter show maternal inheritance) are included. Organellar genes can include mitochondrial genes and apicoplast (when they exist) genes.
3. Phylogentic analyses
Sequence alignment and tree building using the default parameters built into bioinformatic tools is naive, reproaches Morrison. Artifacts may arise from sequence length variation due to indel events, compositional variations like AT content and will not be resolved by multiple analyses (neighbor-joining, max-likelihood etc). Data must not violate the assumptions of the many analyses.
4. Reinterpretation of homologies
The thing about new knowledge is that it must agree or disagree completely or in degrees with old knowledge. Often reinterpretation is essential if we intend to get something worthwhile out of all our research efforts at all. A great example cited by Morrison, and which I spoke about in my previous post is the ineffectiveness of anti-coccidials on Cryptosporidium, easily explained by the genus not belonging to Coccidia.
5. Directed Data Collection
"The collection of pertinent data for the Apicomplexa can be best described as haphazard, which is unlikely to be of much practical value phylogenetically", laments Morrison. He proposes the formation of an informal group which would more likely be able to reach a consensus, over an autocratic formal group or a lackadaisical large group.(Morrison, 2008). I agree with him in that, for any progress from these mires of ignorance, directed data collection is essential.
Some, with adequate reason, have no interest at all in the systemics of taxonomy. Others are absolutely enthralled by the nuances of biological nomenclature. I, being one of the latter, have tried to understand the complexity of the system and have briefly presented the above the way I have understood it. Undoubtedly, the above is not absolute and is subject to change. But, change we will (our understanding and even our knowledge base) when the time comes. Till then, I'll leave you here on the shores of (the land of ) Systemics. So long. Farewell !
References :
1. Adl SM, Simpson AG, Farmer MA, et al. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol 2005;52:399-451.
2. Barta JR, Thompson RC. What is Cryptosporidium? Reappraising its biology and phylogenetic affinities. Trends Parasitol 2006;22:463-468.
3. Cavalier-Smith T. Kingdom protozoa and its 18 phyla. Microbiol Rev 1993;57:953-994.
4. Cavalier-Smith T. A revised six-kingdom system of life. Biol Rev Camb Philos Soc1998;73:203-266.
5. Cox FE. Systematics of the parasitic Protozoa. Trends Parasitol 2002;18:108.
6. Moore RB, Oborník M, Janouskovec J, et al. A photosynthetic alveolate closely related to apicomplexan parasites. Nature 2008;451:959-963.
7. Dimitrov, D., Valkiunas, G., Zehtindjiev, P., Ilieva, M., & Bensch, S. (2013). Molecular characterization of haemosporidian parasites (Haemosporida) in yellow wagtail (Motacilla flava), with description of in vitro ookinetes of Haemoproteus motacillae. Zootaxa, 3666(3), 369–381.
8. Morrison DA. Prospects for elucidating the phylogeny of the Apicomplexa.Parasite. 2008;15(3):191-6.
9. Šlapeta, Jan and Victoria Morin-Adeline. 2011. Apicomplexa Levine 1970. Sporozoa Leucart 1879. Version 18 May 2011. http://tolweb.org/Apicomplexa/2446/2011.05.18 in The Tree of Life Web Project
